Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance.
作者： Hanane Omichessan , Gianluca Severi , Vittorio Perduca
DOI: 10.1371/JOURNAL.PONE.0221235
关键词:
摘要: Mutational signatures refer to patterns in the occurrence of somatic mutations that might be uniquely ascribed particular mutational process. Tumour mutation catalogues can reveal but are often consistent with spectra produced by a variety mutagens. To date, after analysis tens thousands exomes and genomes from about 40 different cancer types, characterized unique probability profile across 96 trinucleotide-based types have been identified, validated catalogued. At same time, several concurrent methods developed for either quantification contribution catalogued given sequence or identification new sample sequences. A review existing computational tools has recently published guide researchers practitioners through their signature analyses, other introduced since its publication and, systematic evaluation comparison performance such is still lacking. In order fill this gap, we carried out an empirical main packages available using both real simulated data. Among results, our study shows more difficult cancers multiple each having small contribution. This work suggests detection based on probabilistic models, especially EMu bayesNMF, general better than NMF-based methods.
harvard.edu
doaj.org参考文章(29)
Daniel D. Lee, H. Sebastian Seung, Learning the parts of objects by non-negative matrix factorization Nature. ,vol. 401, pp. 788- 791 ,(1999) , 10.1038/44565
Xiyue Liao, Mary C. Meyer, coneproj: An R Package for the Primal or Dual Cone Projections with Routines for Constrained Regression Journal of Statistical Software. ,vol. 61, pp. 1- 22 ,(2014) , 10.18637/JSS.V061.I12
Ludmil B. Alexandrov, Serena Nik-Zainal, David C. Wedge, Peter J. Campbell, Michael R. Stratton, Deciphering Signatures of Mutational Processes Operative in Human Cancer Cell Reports. ,vol. 3, pp. 246- 259 ,(2013) , 10.1016/J.CELREP.2012.12.008
Michael R. Stratton, Peter J. Campbell, P. Andrew Futreal, The cancer genome Nature. ,vol. 458, pp. 719- 724 ,(2009) , 10.1038/NATURE07943
V. Y. F. Tan, C. Fevotte, Automatic Relevance Determination in Nonnegative Matrix Factorization with the $(\beta)$-Divergence IEEE Transactions on Pattern Analysis and Machine Intelligence. ,vol. 35, pp. 1592- 1605 ,(2013) , 10.1109/TPAMI.2012.240
Julian S. Gehring, Bernd Fischer, Michael Lawrence, Wolfgang Huber, SomaticSignatures: inferring mutational signatures from single-nucleotide variants Bioinformatics. ,vol. 31, pp. 3673- 3675 ,(2015) , 10.1093/BIOINFORMATICS/BTV408
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel AJR Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolo Bolli, Ake Borg, Anne-Lise Børresen-Dale, Sandrine Boyault, Birgit Burkhardt, Adam P Butler, Carlos Caldas, Helen R Davies, Christine Desmedt, Roland Eils, Jórunn Erla Eyfjörd, John A Foekens, Mel Greaves, Fumie Hosoda, Barbara Hutter, Tomislav Ilicic, Sandrine Imbeaud, Marcin Imielinski, Natalie Jäger, David TW Jones, David Jones, Stian Knappskog, Marcel Kool, Sunil R Lakhani, Carlos López-Otín, Sancha Martin, Nikhil C Munshi, Hiromi Nakamura, Paul A Northcott, Marina Pajic, Elli Papaemmanuil, Angelo Paradiso, John V Pearson, Xose S Puente, Keiran Raine, Manasa Ramakrishna, Andrea L Richardson, Julia Richter, Philip Rosenstiel, Matthias Schlesner, Ton N Schumacher, Paul N Span, Jon W Teague, Yasushi Totoki, Andrew NJ Tutt, Rafael Valdés-Mas, Marit M Van Buuren, Laura van’t Veer, Anne Vincent-Salomon, Nicola Waddell, Lucy R Yates, Australian Pancreatic Cancer Genome Initiative, ICGC Breast Cancer Consortium, Icgc Mmml-Seq Consortium, Icgc PedBrain, Jessica Zucman-Rossi, P Andrew Futreal, Ultan McDermott, Peter Lichter, Matthew Meyerson, Sean M Grimmond, Reiner Siebert, Elías Campo, Tatsuhiro Shibata, Stefan M Pfister, Peter J Campbell, Michael R Stratton, None, Signatures of mutational processes in human cancer Nature. ,vol. 500, pp. 415- 421 ,(2013) , 10.1038/NATURE12477
Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen, EMu: probabilistic inference of mutational processes and their localization in the cancer genome Genome Biology. ,vol. 14, pp. 1- 10 ,(2013) , 10.1186/GB-2013-14-4-R39
Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S. Taylor, Charles Swanton, deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution Genome Biology. ,vol. 17, pp. 31- 31 ,(2016) , 10.1186/S13059-016-0893-4
Maude Ardin, Vincent Cahais, Xavier Castells, Liacine Bouaoun, Graham Byrnes, Zdenko Herceg, Jiri Zavadil, Magali Olivier, MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes BMC Bioinformatics. ,vol. 17, pp. 170- 170 ,(2016) , 10.1186/S12859-016-1011-Z